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Updated QuickStart EukPhylo (markdown)

Godwin Ani 2025-01-24 16:26:52 -05:00
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QuickStart-EukPhylo.md

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# General Steps # General Steps
EukPhylo is composed of two parts, that can be run individually: Part 1 can be run only once, to assign gene families; Part 2 builds MSA, Trees, implement contamination removal and Concatenation. EukPhylo pipeline is composed of two parts, that can be run individually: Part 1 can be run only once, to assign gene families; Part 2 builds MSA, Trees, implement contamination removal and Concatenation.
It's preferable to run Part 2 with the outputs of Part 1, but this is not required as long as the users files are in the same format (one file per species, with sequences name start by 10 digit code and ends with OGx_xxxxxx. See extended version of the wiki for details) It's preferable to run Part 2 with the outputs of Part 1, but this is not required as long as the users files are in the same format (one file per species, with sequences name start by 10 digit code and ends with OGx_xxxxxx. See extended version of the wiki for details)
1. Install EukPhylo 1. Install EukPhylo